# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 08:14:05 2020
#   Inital geometry file: a 100 line input string
#   Ligand name: (3E)-5-fluoro-1-[(6-fluoro-4H-1,3-benzodioxin-8-yl)methyl]-1H-indole-2,3-dione 3-oxime
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O/N=C1/C(=O)N(Cc2cc(F)cc3COCOc23)c4ccc(F)cc14
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 J72  J72  '(3E)-5-fluoro-1-[(6-fluoro-4H-1,3-benzodioxin-8-yl)methyl]-1H-indole-2,3-dione 3-oxime'  ligand  37  25  .  2022-07-25  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_J72
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 J72  O1    O  OH1   0  -0.510  -3.8557  -1.8067  -1.9579
 J72  N2    N  N     0  -0.076  -2.6948  -2.2311  -1.4484
 J72  C3    C  CR5   0   0.011  -2.1930  -1.4372  -0.5896
 J72  C4    C  CR5   0   0.537  -0.8904  -1.8027   0.0548
 J72  O5    O  O     0  -0.430  -0.2262  -2.8002  -0.1135
 J72  N6    N  NR5   0  -0.622  -0.5920  -0.7734   0.8998
 J72  C7    C  CH2   0  -0.407   0.6074  -0.7661   1.7108
 J72  C8    C  CR6   0   0.036   1.8651  -0.6251   0.8951
 J72  C9    C  CR16  0  -0.469   2.8144  -1.6354   0.8804
 J72  C10   C  CR6   0   0.535   3.9711  -1.4697   0.1422
 J72  F11   F  F     0  -0.320   4.8870  -2.4551   0.1419
 J72  C12   C  CR16  0  -0.459   4.2078  -0.3367  -0.6043
 J72  C13   C  CR6   0  -0.064   3.2582   0.6776  -0.6067
 J72  C14   C  CH2   0  -0.192   3.4419   1.9289  -1.4207
 J72  O15   O  O2    0  -0.473   2.2229   2.6382  -1.5214
 J72  C16   C  CH2   0   0.027   1.6111   2.7585  -0.2846
 J72  O17   O  O2    0  -0.479   1.1614   1.5055   0.1852
 J72  C18   C  CR6   0   0.366   2.1011   0.5318   0.1518
 J72  C19   C  CR56  0   0.409  -1.5869   0.2059   0.8709
 J72  C20   C  CR16  0  -0.275  -1.6638   1.3814   1.5907
 J72  C21   C  CR16  0  -0.414  -2.7742   2.1983   1.4008
 J72  C22   C  CR6   0   0.536  -3.7619   1.8258   0.5090
 J72  F23   F  F     0  -0.319  -4.8245   2.6332   0.3458
 J72  C24   C  CR16  0  -0.476  -3.7040   0.6537  -0.2237
 J72  C25   C  CR56  0   0.041  -2.5976  -0.1590  -0.0296
 J72  HO1   H  HOH1  0   0.496  -4.1162  -2.4859  -2.5925
 J72  H7    H  HCH2  0   0.295   0.5224   0.0465   2.4313
 J72  H7A   H  HCH2  0   0.295   0.6475  -1.6902   2.2889
 J72  H9    H  HCR6  0   0.278   2.6542  -2.5447   1.4459
 J72  H12   H  HCR6  0   0.282   5.1141  -0.2446  -1.1913
 J72  H14   H  HCH2  0   0.246   4.2230   2.5612  -0.9792
 J72  H14A  H  HCH2  0   0.267   3.7539   1.6821  -2.4362
 J72  H16   H  HCH2  0   0.220   2.2928   3.1988   0.4571
 J72  H16A  H  HCH2  0   0.249   0.7278   3.3834  -0.3944
 J72  H20   H  HCR6  0   0.285  -0.8916   1.6829   2.2837
 J72  H21   H  HCR6  0   0.289  -2.8617   3.1261   1.9504
 J72  H24   H  HCR6  0   0.285  -4.4977   0.3984  -0.9107

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 J72  N2   O1    single    1.337  0.020  1.337
 J72  O1   HO1   single    0.850  0.020  0.980
 J72  C3   N2    double    1.273  0.020  1.273
 J72  C4   C3    single    1.499  0.020  1.499
 J72  C25  C3    single    1.453  0.020  1.453
 J72  N6   C4    single    1.365  0.020  1.365
 J72  O5   C4    double    1.210  0.020  1.210
 J72  C7   N6    single    1.448  0.020  1.448
 J72  N6   C19   single    1.396  0.020  1.396
 J72  C7   C8    single    1.506  0.020  1.506
 J72  C7   H7    single    0.970  0.020  1.090
 J72  C7   H7A   single    0.970  0.020  1.090
 J72  C18  C8    aromatic  1.395  0.020  1.395
 J72  C8   C9    aromatic  1.386  0.020  1.386
 J72  C9   C10   aromatic  1.382  0.020  1.382
 J72  C9   H9    single    0.930  0.020  1.080
 J72  C12  C10   aromatic  1.377  0.020  1.377
 J72  C10  F11   single    1.345  0.020  1.345
 J72  C13  C12   aromatic  1.389  0.020  1.389
 J72  C12  H12   single    0.930  0.020  1.080
 J72  C18  C13   aromatic  1.391  0.020  1.391
 J72  C14  C13   single    1.504  0.020  1.504
 J72  O15  C14   single    1.414  0.020  1.414
 J72  C14  H14   single    0.970  0.020  1.090
 J72  C14  H14A  single    0.970  0.020  1.090
 J72  C16  O15   single    1.385  0.020  1.385
 J72  O17  C16   single    1.412  0.020  1.412
 J72  C16  H16   single    0.970  0.020  1.090
 J72  C16  H16A  single    0.970  0.020  1.090
 J72  O17  C18   single    1.354  0.020  1.354
 J72  C20  C19   aromatic  1.380  0.020  1.380
 J72  C19  C25   aromatic  1.402  0.020  1.402
 J72  C20  C21   aromatic  1.392  0.020  1.392
 J72  C20  H20   single    0.930  0.020  1.080
 J72  C21  C22   aromatic  1.382  0.020  1.382
 J72  C21  H21   single    0.930  0.020  1.080
 J72  C22  C24   aromatic  1.383  0.020  1.383
 J72  C22  F23   single    1.344  0.020  1.344
 J72  C25  C24   aromatic  1.386  0.020  1.386
 J72  C24  H24   single    0.930  0.020  1.080

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 J72  HO1   O1   N2   105.15  3.000
 J72  C3    N2   O1   113.67  3.000
 J72  C25   C3   C4   106.91  3.000
 J72  C25   C3   N2   134.36  3.000
 J72  C4    C3   N2   118.73  3.000
 J72  N6    C4   O5   126.00  3.000
 J72  O5    C4   C3   128.19  3.000
 J72  N6    C4   C3   105.81  3.000
 J72  C19   N6   C7   126.75  3.000
 J72  C19   N6   C4   111.12  3.000
 J72  C7    N6   C4   122.12  3.000
 J72  H7A   C7   H7   106.51  3.000
 J72  H7A   C7   C8   109.62  3.000
 J72  H7    C7   C8   110.71  3.000
 J72  H7A   C7   N6   108.85  3.000
 J72  H7    C7   N6   108.04  3.000
 J72  C8    C7   N6   112.90  3.000
 J72  C18   C8   C9   118.87  3.000
 J72  C9    C8   C7   120.63  3.000
 J72  C18   C8   C7   120.50  3.000
 J72  H9    C9   C10  120.24  3.000
 J72  H9    C9   C8   120.34  3.000
 J72  C10   C9   C8   119.43  3.000
 J72  C12   C10  F11  119.04  3.000
 J72  F11   C10  C9   118.82  3.000
 J72  C12   C10  C9   122.14  3.000
 J72  H12   C12  C13  120.57  3.000
 J72  H12   C12  C10  120.48  3.000
 J72  C13   C12  C10  118.94  3.000
 J72  C18   C13  C14  118.93  3.000
 J72  C14   C13  C12  121.65  3.000
 J72  C18   C13  C12  119.41  3.000
 J72  H14A  C14  H14  107.53  3.000
 J72  H14A  C14  O15  107.09  3.000
 J72  H14   C14  O15  110.68  3.000
 J72  H14A  C14  C13  110.53  3.000
 J72  H14   C14  C13  110.40  3.000
 J72  O15   C14  C13  110.53  3.000
 J72  C16   O15  C14  111.15  3.000
 J72  H16A  C16  H16  109.97  3.000
 J72  H16A  C16  O17  106.55  3.000
 J72  H16   C16  O17  109.17  3.000
 J72  H16A  C16  O15  108.58  3.000
 J72  H16   C16  O15  111.31  3.000
 J72  O17   C16  O15  111.15  3.000
 J72  C18   O17  C16  114.15  3.000
 J72  O17   C18  C13  121.03  3.000
 J72  O17   C18  C8   117.77  3.000
 J72  C13   C18  C8   121.20  3.000
 J72  C25   C19  C20  121.09  3.000
 J72  C25   C19  N6   110.15  3.000
 J72  C20   C19  N6   128.76  3.000
 J72  H20   C20  C21  119.61  3.000
 J72  H20   C20  C19  122.15  3.000
 J72  C21   C20  C19  118.24  3.000
 J72  H21   C21  C22  120.08  3.000
 J72  H21   C21  C20  119.91  3.000
 J72  C22   C21  C20  120.01  3.000
 J72  C24   C22  F23  118.52  3.000
 J72  F23   C22  C21  118.78  3.000
 J72  C24   C22  C21  122.70  3.000
 J72  H24   C24  C25  122.46  3.000
 J72  H24   C24  C22  120.41  3.000
 J72  C25   C24  C22  117.12  3.000
 J72  C24   C25  C19  120.84  3.000
 J72  C24   C25  C3   133.15  3.000
 J72  C19   C25  C3   106.01  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 J72  CONST_01  C12  C13  C18  C8     0.00   0.0  0
 J72  CONST_02  C12  C10  C9   C8     0.00   0.0  0
 J72  CONST_03  C13  C18  C8   C9     0.00   0.0  0
 J72  CONST_04  C13  C12  C10  C9     0.00   0.0  0
 J72  CONST_05  C18  C8   C9   C10    0.00   0.0  0
 J72  CONST_06  C18  C13  C12  C10    0.00   0.0  0
 J72  CONST_07  C22  C21  C20  C19    0.00   0.0  0
 J72  CONST_08  C22  C24  C25  C19    0.00   0.0  0
 J72  CONST_09  C24  C25  C19  C20    0.00   0.0  0
 J72  CONST_10  C24  C22  C21  C20    0.00   0.0  0
 J72  CONST_11  C25  C19  C20  C21    0.00   0.0  0
 J72  CONST_12  C25  C24  C22  C21    0.00   0.0  0
 J72  CONST_13  C19  N6   C4   C3     0.00   0.0  0
 J72  CONST_14  C13  C18  C8   C7   180.00   0.0  0
 J72  CONST_15  O17  C18  C8   C7     0.00   0.0  0
 J72  CONST_16  C10  C9   C8   C7   180.00   0.0  0
 J72  CONST_17  F11  C10  C9   C8   180.00   0.0  0
 J72  CONST_18  C13  C12  C10  F11  180.00   0.0  0
 J72  CONST_19  F23  C22  C21  C20  180.00   0.0  0
 J72  CONST_20  C25  C24  C22  F23  180.00   0.0  0
 J72  CONST_21  C7   N6   C4   C3   180.00   0.0  0
 J72  CONST_22  C19  N6   C4   O5   180.00   0.0  0
 J72  CONST_23  H24  C24  C25  C3     0.00   0.0  0
 J72  CONST_24  H20  C20  C19  N6     0.00   0.0  0
 J72  CONST_25  H12  C12  C10  C9   180.00   0.0  0
 J72  CONST_26  H9   C9   C10  C12  180.00   0.0  0
 J72  CONST_27  H21  C21  C20  C19  180.00   0.0  0
 J72  CONST_28  C7   N6   C4   O5     0.00   0.0  0
 J72  Var_01    O15  C14  C13  C12  165.43  30.0  1
 J72  Var_02    O17  C16  O15  C14  -68.09  30.0  1
 J72  Var_03    C8   C7   N6   C4    68.26  30.0  2
 J72  Var_04    C18  C8   C7   N6    63.71  30.0  2
 J72  Var_05    C4   C3   N2   O1   179.99  30.0  2

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 J72  plan-1  N2   0.020
 J72  plan-1  C3   0.020
 J72  plan-1  C4   0.020
 J72  plan-1  O5   0.020
 J72  plan-1  N6   0.020
 J72  plan-1  C7   0.020
 J72  plan-1  C19  0.020
 J72  plan-1  C20  0.020
 J72  plan-1  C21  0.020
 J72  plan-1  C22  0.020
 J72  plan-1  F23  0.020
 J72  plan-1  C24  0.020
 J72  plan-1  C25  0.020
 J72  plan-1  H20  0.020
 J72  plan-1  H21  0.020
 J72  plan-1  H24  0.020
 J72  plan-2  C7   0.020
 J72  plan-2  C8   0.020
 J72  plan-2  C9   0.020
 J72  plan-2  C10  0.020
 J72  plan-2  F11  0.020
 J72  plan-2  C12  0.020
 J72  plan-2  C13  0.020
 J72  plan-2  C14  0.020
 J72  plan-2  O17  0.020
 J72  plan-2  C18  0.020
 J72  plan-2  H9   0.020
 J72  plan-2  H12  0.020

